Beyond the Africa Cup, I know that there are other important regional championships in Africa. I think that the most important is the CECAFA Cup, but what is the actual situation of these other championships ( WAFU Cup, Amilcar Cabral Cup, COSAFA Cup and CEMAC Cup ) ?
I think a lot of the regional tournaments are going by the wayside. African countries are constantly busy with either World Cup Qualifying or African Cup of Nations qualifying - there just isn't time to also have a regional tournament too. Plus a lot of teams are strapped for cash, and Africa is a very large continent, so it's not like they can easily afford to travel. Senegal and Gambia withdrew from the last WAFU Cup (that was actually held) because it was hosted in Nigeria, way too far away for them to go for such an "unimportant" competition.
CECAFA is still alive and is the oldest existing African tournament. I think it goes back to the 1930s when it was called the Gossage cup http://www.cecafafootball.org/
Kenya has won the 2013 CECAFA cup. Sudan were second and Zambia finished 3rd http://www.bbc.com/sport/0/football/25358196
i think the CHAN a step is the right direction for improving domestic football in the continent, especially since most regional championships have become defunct. do not forget that there are several arab championships and tournaments that north african nations compete it aswell